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                            <h2>
                                TCGA Center for Systems Analysis of the Cancer Regulome
                                <small>
                                    <p>
                                        <a href="http://www.systemsbiology.org" target="_blank">Institute for Systems Biology</a> and
                                        <a href="http://www.mdanderson.org" target="_blank">MD Anderson Cancer Center</a>
                                    </p>
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                            </h2>
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                        <p>
                            The Cancer Genome Atlas (TCGA) provides an unprecedented opportunity to take an integrated approach
                            toward a systems level understanding of regulatory disruptions in cancer. Such disruptions and their
                            consequences are intertwined within complex dynamical networks through a multitude of interactions
                            among different types of biomolecules. Understanding such relationships requires multivariate analysis
                            methods that can be effective in the context of highly heterogeneous data, measurement uncertainty,
                            and missing data.
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                    <div class="carousel slide" id="homeCarousel">
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                                <a href="http://www.cell.com/cancer-cell/issue?pii=S1535-6108(13)X0003-0" target="_blank">
                                    <img src="images/cancer_cell_cover.jpg" width="192" height="250" alt="Cover of Cancer Cell">
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                                <div class="carousel-caption">
                                    <p>The cover of Cancer Cell features the <a href="http://www.sciencedirect.com/science/article/pii/S1535610813000032" target="_blank">paper</a>: 
                                    Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer</p>
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                                <a href="http://explorer.cancerregulome.org/all_pairs/" target="_blank">
                                    <img src="images/regulome_explorer.png" width="500" height="250" alt="Regulome Explorer">
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                                    <p>Regulome Explorer: Explore, mine, and visualize complex datasets</p>
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                                <a href="http://explorer.cancerregulome.org/pubcrawl/" target="_blank">
                                    <img src="images/pubcrawl.png" width="500" height="250" alt="Pubcrawl">
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                                    <p>Pubcrawl: Dynamic network topologies created from literature distances</p>
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                                <a href="http://explorer.cancerregulome.org/crc_agg/" target="_blank">
                                    <img src="images/crc_aggressiveness.png" width="500" height="250" alt="Pubcrawl">
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                                    <p>CRC Aggressiveness: Explore features related to colorectal cancer aggressiveness</p>
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                                <a href="http://genespot.cancerregulome.org/" target="_blank">
                                    <img src="images/genespot.png" width="500" height="250" alt="GeneSpot">
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                                    <p>GeneSpot: Explore TCGA data from a Gene-centric point-of-view</p>
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                            <h2>Research</h2>
                            <p>Development of novel computational approaches for analyzing large-scale heterogeneous data.</p>
                            <p><a class="btn" href="research.html">View Details &raquo;</a></p>
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                            <h2>Cancer Studies</h2>
                            <p>Actively participating and contributing to several TCGA tumor Analysis Working Groups.</p>
                            <p><a class="btn" href="cancerstudies.html">View Details &raquo;</a></p>
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                            <h2>Software</h2>
                            <p>Web-based interactive visualization and exploratory tools, and computational infrastructure that promotes collaborative research.</p>
                            <p><a class="btn" href="software.html">View Details &raquo;</a></p>
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                            <h3>News & Events</h3>
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                            <h4>February 2013</h4>
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                                <div class="text">
                                    <a href="http://www.sciencedirect.com/science/article/pii/S1535610813000032" target="_blank">New paper</a> published in Cancer Cell on "Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer" as part of the <a href="http://cancergenome.nih.gov/" target="_blank">The Cancer Genome Atlas</a>(TCGA) project.
                                    <br/><br/>
                                    The <a href="http://www.cell.com/cancer-cell/issue?pii=S1535-6108(13)X0003-0#">cover of Cancer Cell</a> features the article, with a graphic depicting the analysis.
                                </div>
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                        <hr/>
                           <div>
                            <h4>November 2012</h4>
                            <div class="sideEventsCell">
                                <div class="text">
                                    The Center for Systems Analysis of the Cancer Regulome attended the 2nd Annual TCGA Scientific Symposium. The symposium was co-chaired by Ilya Shmulevich.
                                    <br/><br/>
                                    Brady Bernard and Hector Rovira gave a <a href="http://cancergenome.nih.gov/newsevents/multimedialibrary/videos/GeneSpotBernard2012">talk</a>, introducing <a href="http://www.genespot.org">Genespot</a>: A Portal for Interactive Gene-Centric Exploration of The Cancer Genome Atlas.
                                    <br/><br/>
                                    Dick Kreisberg presented a <a href="http://bit.ly/regex_workshop">workshop</a> on the Regulome Explorer.
                                    
                                </div>
                            </div>
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                        <hr/>
                                <div>
                            <h4>October 2012</h4>
                            <div class="sideEventsCell">
                                <div class="text">
                                    <a href="http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html" target="_blank">New paper</a> published in Nature on comprehensive molecular portraits of human breast tumors as a part of <a href="http://cancergenome.nih.gov/" target="_blank">The Cancer Genome Atlas</a>(TCGA) project.
                                    <br/><br/>
                                    An <a href="http://www.nytimes.com/2012/09/24/health/study-finds-variations-of-breast-cancer.html" target="_blank">article</a> related to the work was published in the New York Times.
                                </div>
                            </div>
                        </div>
                        <hr/>
                          <div>
                            <h4>September 2012</h4>
                            <div class="sideEventsCell">
                                <div class="text">
                                    <a href="http://cancergenome.nih.gov/researchhighlights/tcgainaction/CloudMayWidenBottleneck" target="_blank">A recent article</a> on the Shmulevich Group's efforts to analyze genomic information using large computational clusters with cloud infrastructure on demand.
                                </div>
                            </div>
                        </div>
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                        <div class="page">
                        <div>
                            <h4>July 2012</h4>
                            <div class="sideEventsCell">
                                <div class="text">
                                    <a href="http://www.nature.com/nature/journal/v487/n7407/full/nature11252.html" target="_blank">New paper</a> published in Nature on Colorectal cancer characterization as a part of <a href="http://cancergenome.nih.gov/" target="_blank">The Cancer Genome Atlas</a>(TCGA) project.
                                    <br/><br/>
                                    An <a href="http://www.nytimes.com/2012/07/19/health/research/vast-gene-study-raises-hopes-for-colon-cancer-drugs.html" target="_blank">article</a> related to the work was featured on the home page of the New York Times.
                                </div>
                            </div>
                        </div>
                        <hr/>
                        <div>
                            <h4>June 2012</h4>
                            <div class="sideEventsCell">
                                <div class="text">
                                    Our work was featured during a <a href="https://developers.google.com/compute/io" target="_blank">keynote presentation at the Google I/O 2012 conference</a>.
                                    <br/><br/>
                                    The keynote, delivered by Urs Hölzle, Senior Vice President of Infrastructure at Google,
                                    introduced Google Compute Engine. He demonstrated how
                                    <a href="http://rf-ace.googlecode.com" target="_blank">RF-ACE</a>, a machine learning
                                    algorithm that learns associations among genomic and clinical features, can be scaled to
                                    600,000 cores across Google’s global data centers and the results visualized using a version of
                                    <a href="http://explorer.cancerregulome.org" target="_blank">Regulome Explorer</a>.
                                    <br/><br/>
                                    A case study written by Google can be found <a href="downloads/ComputeISBCaseStudy.pdf" target="_blank">here</a>.
                                </div>
                            </div>
                        </div>
                        <hr/>
                            <div>
                            <h4>May 2012</h4>
                            <div class="sideEventsCell">
                                <div class="text">
                                    <a href="http://explorer.cancerregulome.org/" target="_blank">Regulome Explorer</a> is featured in
                                    <a href="http://www.genengnews.com/gen-articles/mathematics-transforming-bioresearch/4098/" target="_blank">this article</a>
                                    where <a href="https://www.systemsbiology.org/leroy-hood" target="_blank">ISB founder Dr. Leroy Hood</a> talks about
                                    the application of mathematics to biological research.
                                </div>
                                <div class="image">
                                    <a href="http://www.genengnews.com/gen-articles/mathematics-transforming-bioresearch/4098/" target="_blank">
                                        <img src="http://www.genengnews.com/App_Themes/Public/Images/genlogo_footer.gif">
                                    </a>
                                </div>
                            </div>
                        </div>
                        <hr/>
                        <div>
                            <h4>March 2012</h4>
                            <div class="sideEventsCell">
                                <div class="text">
                                    <a href="http://explorer.cancerregulome.org/" target="_blank">Regulome Explorer</a> is covered in
                                    <a href="http://the-scientist.com/2012/03/01/combing-the-cancer-genome/" target="_blank">this story</a>
                                    about online tools available for analyzing TCGA data.
                                </div>
                                <div class="image">
                                    <a href="http://the-scientist.com/2012/03/01/combing-the-cancer-genome/" target="_blank">
                                        <img src="images/TheScientistlogo.magazine.jpg">
                                    </a>
                                </div>
                            </div>
                        </div>
                        </div>
                        <div class="page">
                        <div>
                            <h4>December 2011</h4>
                            <div class="sideEventsCell">
                                <div class="text">
                                    <a href="http://addama.googlecode.com" target="_blank">Addama</a> described in this
                                    <a href="http://www.nature.com/nmeth/journal/v9/n1/full/nmeth.1815.html" target="_blank">technology feature</a>
                                    on adaptive technologies for systems biology data integration.
                                </div>
                                <div class="image">
                                    <a href="http://www.nature.com/nmeth/journal/v9/n1/full/nmeth.1815.html" target="_blank">
                                        <img src="images/nmeth_logo.png">
                                    </a>
                                </div>
                            </div>
                        </div>
                        <hr/>
                        <div>
                            <h4>October 2011</h4>
                            <div class="sideEventsCell">
                                <div class="text">
                                    <a href="http://jama.jamanetwork.com/article.aspx?articleid=1104495" target="_blank">New paper</a>
                                    published in the Journal of the American Medical Association showing that women with high-grade
                                    ovarian cancer live longer and respond better to platinum-based chemotherapy when their tumors
                                    have BRCA2 genetic mutations.
                                    <br/>
                                    <br/>
                                    There was also an <a href="http://jama.jamanetwork.com/article.aspx?articleid=1104489" target="_blank">editorial</a> published in JAMA.
                                </div>
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                                    <a href="http://jama.jamanetwork.com/article.aspx?articleid=1104495" target="_blank">
                                        <img src="images/jama_logo.gif">
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